General information for g2222.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein Optix.
Parent gene
- The parent gene g2222 is located on chr_3: 16074613..16094856 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g2222 | g2222.t1 | TSS | g2222.t1 | 16074011 | 16074011 |
| chr_3 | g2222 | g2222.t1 | isoform | g2222.t1 | 16074613 | 16094856 |
| chr_3 | g2222 | g2222.t1 | exon | g2222.t1.exon1 | 16074613 | 16075101 |
| chr_3 | g2222 | g2222.t1 | cds | g2222.t1.CDS1 | 16074613 | 16075101 |
| chr_3 | g2222 | g2222.t1 | exon | g2222.t1.exon2 | 16075165 | 16075241 |
| chr_3 | g2222 | g2222.t1 | cds | g2222.t1.CDS2 | 16075165 | 16075241 |
| chr_3 | g2222 | g2222.t1 | exon | g2222.t1.exon3 | 16076102 | 16076220 |
| chr_3 | g2222 | g2222.t1 | cds | g2222.t1.CDS3 | 16076102 | 16076220 |
| chr_3 | g2222 | g2222.t1 | exon | g2222.t1.exon4 | 16076309 | 16076567 |
| chr_3 | g2222 | g2222.t1 | cds | g2222.t1.CDS4 | 16076309 | 16076567 |
| chr_3 | g2222 | g2222.t1 | exon | g2222.t1.exon5 | 16093876 | 16094177 |
| chr_3 | g2222 | g2222.t1 | cds | g2222.t1.CDS5 | 16093876 | 16094177 |
| chr_3 | g2222 | g2222.t1 | exon | g2222.t1.exon6 | 16094261 | 16094856 |
| chr_3 | g2222 | g2222.t1 | cds | g2222.t1.CDS6 | 16094261 | 16094856 |
| chr_3 | g2222 | g2222.t1 | TTS | g2222.t1 | NA | NA |
Sequences
>g2222.t1 Gene=g2222 Length=1842
ATGGCCGTGGTTGGGCCCAATAACGGAATCGTCATACCAACCGCAATCAGGCGATCAATA
ACACCACAGCCGTCGATTATTCAGGAGTCTGTGACACTATTGAATTCGACATCGCCGAGC
TCTTCTGTTTCACCGCCGCCGCATAGTGAAACAAATTTAGGACAAAATAGTAGTGGCAAT
AATAATAATAATAGTAATGATAATAATAATACGCCTAGTGTGAATAATAACAATTTAATA
GCAAATTCACCTCAAATGCATCCACATTATGGTCATCCGCCACACCATCACGGGCATCAT
GGACATCCACAGCCTCATCATTTTCACAGTCACCCGCATCATCCTATTCTAGCACCTAGT
CCTCTTTTCGCCTTACCTACTTTAAATTTTACCGCTGGCCAAGTTGCCACAGTTTGTGAA
ACTTTAGAGGAATCAGGTGATATTGAGCGATTAGCTAGATTTCTTTGGAGCCTTCCCGTT
GCACATCCGAATATCACTGAATTGGATCGATCAGAAGCTGTACTACGTGCTCGTGCTGTC
GTTGCCTACCATACTGGACATTTTAGAGAGCTATATGCAATTTTGGAGCGACATAAATTT
ACAAAAGGTTCGCATGGTAAATTACAAGCGATGTGGCTAGAGGCACACTATCATGAGGCA
GAAAAATTGCGTGGTCGACCCCTCGGTCCCGTCGATAAATACCGTGTGAGAAAGAAGTTT
CCATTACCGCGTACAATTTGGGATGGTGAACAGAAAACGCACTGTTTCAAGGAACGAACT
CGTAGTTTATTGCGTGAGTGGTACTTGCAAGATCCATATCCAAATCCAACAAAGAAACGA
GAATTGGCATCTGCTACAGGCCTAACACCGACACAAGTTGGCAATTGGTTTAAAAATCGA
CGACAACGTGATAGAGCGGCAGCAGCGAAAAATAGAAGTCATGGATTAAATCAACCGCCA
ATGTCCGGAAGCAATTCAGGCAATCTGAGTGGACGTCATTTGCATCCCACATTGTCGCCC
GACACAGATTCTGATAGTGACTCAGATATATCACTTGGTACACATTCACCAATTCCGTCA
ATGGCATCACAACATAGTCCAAACTCTAGCTCTGGTCTAAATGATCGTGATCTAGAACAA
CTTGCTGAACAACATAGAGACTCGCGTGGCGAGGCAGATTATCGAAATTTCGCATCGTTA
CAATCATTTCGATTCGGTGAACATCTAAATGTTGCTGGATTTACAAATGCATTCAGTAGA
CAGTTTTTACCGAGCATGCCTTATCGTATGAATGATAATACATCACCACCAAATCATTCG
CCACCAATTGGCGTTACACCATCGACATCACAAACTGGAACCTCAACAACATTATCACAA
TCTCAATCAGCTTACAGTTTACCAGTCGGTCTTATTCGTCCTCAACCTCAACTGCCACAG
AATGCCGCTATATCCGCGATGGTAGCAGCATGTGTCGCCAACGGTCAACAACCGAATGGA
AGTCCAAATCAGACACTCCTTCAACATCACTTGAATCAACAAGCAGCAGCAGCTGCCGCA
GCGCAAATATCTCCATTGAGAATACGAATAAATTCACCCACACGAATCAACTCAACATCG
TCGGCATCTCAAGCGTCGTCGAATGATGTCATTACAACGACATCATCAAGTCCAACTGTT
CCCGGAACGACATTATTGCCGTCGCACAAGCACTCGCTAATTCTAAATGGAGGTCATTTA
GCAAGAATGTCACAAATGAGTCAACTTCATCGTCCTTTTGAATCGCCCTCGCCACCATTG
TCAGCAGTGCAATCAAATAGAGCGGCTAAAGAGAGCTCGTGA
>g2222.t1 Gene=g2222 Length=613
MAVVGPNNGIVIPTAIRRSITPQPSIIQESVTLLNSTSPSSSVSPPPHSETNLGQNSSGN
NNNNSNDNNNTPSVNNNNLIANSPQMHPHYGHPPHHHGHHGHPQPHHFHSHPHHPILAPS
PLFALPTLNFTAGQVATVCETLEESGDIERLARFLWSLPVAHPNITELDRSEAVLRARAV
VAYHTGHFRELYAILERHKFTKGSHGKLQAMWLEAHYHEAEKLRGRPLGPVDKYRVRKKF
PLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELASATGLTPTQVGNWFKNR
RQRDRAAAAKNRSHGLNQPPMSGSNSGNLSGRHLHPTLSPDTDSDSDSDISLGTHSPIPS
MASQHSPNSSSGLNDRDLEQLAEQHRDSRGEADYRNFASLQSFRFGEHLNVAGFTNAFSR
QFLPSMPYRMNDNTSPPNHSPPIGVTPSTSQTGTSTTLSQSQSAYSLPVGLIRPQPQLPQ
NAAISAMVAACVANGQQPNGSPNQTLLQHHLNQQAAAAAAAQISPLRIRINSPTRINSTS
SASQASSNDVITTTSSSPTVPGTTLLPSHKHSLILNGGHLARMSQMSQLHRPFESPSPPL
SAVQSNRAAKESS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2222.t1 | CDD | cd00086 | homeodomain | 251 | 299 | 4.87444E-12 |
| 6 | g2222.t1 | Gene3D | G3DSA:1.10.10.60 | - | 248 | 316 | 6.5E-17 |
| 9 | g2222.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 36 | 56 | - |
| 14 | g2222.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 92 | 112 | - |
| 10 | g2222.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 292 | 328 | - |
| 15 | g2222.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 356 | 375 | - |
| 12 | g2222.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 534 | 565 | - |
| 13 | g2222.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 586 | 613 | - |
| 11 | g2222.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 588 | 613 | - |
| 3 | g2222.t1 | PANTHER | PTHR10390:SF33 | PROTEIN OPTIX | 105 | 556 | 1.5E-131 |
| 4 | g2222.t1 | PANTHER | PTHR10390 | HOMEOBOX PROTEIN SIX | 105 | 556 | 1.5E-131 |
| 1 | g2222.t1 | Pfam | PF16878 | Transcriptional regulator, SIX1, N-terminal SD domain | 130 | 244 | 9.8E-47 |
| 2 | g2222.t1 | Pfam | PF00046 | Homeodomain | 254 | 305 | 9.3E-12 |
| 16 | g2222.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 247 | 307 | 14.56 |
| 8 | g2222.t1 | SMART | SM00389 | HOX_1 | 250 | 311 | 1.1E-13 |
| 5 | g2222.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 247 | 315 | 3.01E-16 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003677 | DNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K19473 (homeobox protein SIX3/6)
Pathway
This gene does not belong to any pathways.
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed